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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.1 Publication

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.1 Publication

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.1 Publication
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei15SubstrateCombined sources1 Publication1
Binding sitei74SubstrateUniRule annotation1
Active sitei83Proton donorCombined sources1 Publication1
Binding sitei159SubstrateCombined sources1 Publication1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei194SubstrateCombined sources1 Publication1
Sitei212Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei221Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciCORYNE:G18NG-11535-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase1 Publication (EC:5.1.1.71 Publication)
Short name:
DAP epimerase1 Publication
Alternative name(s):
PLP-independent amino acid racemase1 Publication
Gene namesi
Name:dapF1 Publication
Ordered Locus Names:Cgl1943, cg2129
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000000582 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene are unable transform L,L-DAP and show an impaired growth when supplied with low ammonium but high concentrations of carbon.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498371 – 277Diaminopimelate epimeraseAdd BLAST277

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi196627.cg2129.

Structurei

Secondary structure

1277
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 12Combined sources10
Beta strandi15 – 21Combined sources7
Helixi31 – 38Combined sources8
Turni40 – 42Combined sources3
Beta strandi47 – 54Combined sources8
Helixi55 – 57Combined sources3
Beta strandi67 – 74Combined sources8
Helixi86 – 96Combined sources11
Beta strandi99 – 108Combined sources10
Beta strandi114 – 121Combined sources8
Beta strandi123 – 131Combined sources9
Beta strandi136 – 145Combined sources10
Beta strandi148 – 165Combined sources18
Helixi171 – 176Combined sources6
Turni186 – 188Combined sources3
Beta strandi194 – 198Combined sources5
Beta strandi205 – 212Combined sources8
Turni213 – 215Combined sources3
Helixi222 – 235Combined sources14
Beta strandi239 – 247Combined sources9
Beta strandi250 – 257Combined sources8
Beta strandi260 – 277Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5H2GX-ray2.00A/B1-277[»]
5H2YX-ray2.00A/B1-277[»]
5M47X-ray2.59A1-277[»]
ProteinModelPortaliQ8NP73.
SMRiQ8NP73.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni84 – 85Substrate bindingCombined sources1 Publication2
Regioni212 – 213Substrate bindingCombined sources1 Publication2
Regioni222 – 223Substrate bindingCombined sources1 Publication2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMCGNGGR.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiView protein in PROSITE
PS01326. DAP_EPIMERASE. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8NP73-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNLTIPFAKG HATENDFIII PDEDARLDLT PEMVVTLCDR RAGIGADGIL
60 70 80 90 100
RVVKAADVEG STVDPSLWFM DYRNADGSLA EMCGNGVRLF AHWLYSRGLV
110 120 130 140 150
DNTSFDIGTR AGVRHVDILQ ADQHSAQVRV DMGIPDVTGL STCDINGQVF
160 170 180 190 200
AGLGVDMGNP HLACVVPGLS ASALADMELR APTFDQEFFP HGVNVEIVTE
210 220 230 240 250
LEDDAVSMRV WERGVGETRS CGTGTVAAAC AALADAGLGE GTVKVCVPGG
260 270
EVEVQIFDDG STLTGPSAII ALGEVQI
Length:277
Mass (Da):29,203
Last modified:October 25, 2002 - v1
Checksum:i41458032D8C7E9DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB99336.1.
BX927153 Genomic DNA. Translation: CAF20284.1.
RefSeqiNP_601150.1. NC_003450.3.
WP_011014772.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB99336; BAB99336; BAB99336.
CAF20284; CAF20284; cg2129.
GeneIDi1019900.
KEGGicgb:cg2129.
cgl:NCgl1868.
PATRICifig|196627.13.peg.1881.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB99336.1.
BX927153 Genomic DNA. Translation: CAF20284.1.
RefSeqiNP_601150.1. NC_003450.3.
WP_011014772.1. NC_006958.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5H2GX-ray2.00A/B1-277[»]
5H2YX-ray2.00A/B1-277[»]
5M47X-ray2.59A1-277[»]
ProteinModelPortaliQ8NP73.
SMRiQ8NP73.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg2129.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB99336; BAB99336; BAB99336.
CAF20284; CAF20284; cg2129.
GeneIDi1019900.
KEGGicgb:cg2129.
cgl:NCgl1868.
PATRICifig|196627.13.peg.1881.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
KOiK01778.
OMAiMCGNGGR.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciCORYNE:G18NG-11535-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiView protein in InterPro
IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiView protein in Pfam
PF01678. DAP_epimerase. 2 hits.
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiView protein in PROSITE
PS01326. DAP_EPIMERASE. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_CORGL
AccessioniPrimary (citable) accession number: Q8NP73
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2002
Last sequence update: October 25, 2002
Last modified: June 7, 2017
This is version 89 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.